Histoplasma capsulatum is a dimorphic fungal pathogen capable of causing acute pulmonary disease in otherwise healthy individuals and lethal disease in immunocompromised humans (Ampel, 1996, Emerg. Infect. Dis., 2: 109–116; Eissenberg, 1994, The Interplay Between Histoplasma Capsulatum and Its Host Cells, Vol, I, Ch. 6, W. B. Saunders Company, Ltd. London, UK; Wheat et al., 1985, Am. J. Med., 78: 203–210). In its most serious form, the infection disseminates throughout the body. Disseminated histoplasmosis, coinciding with laboratory evidence of HIV infection, is regarded sufficient for a diagnosis of AIDS (Castro et al., 1992, MMRW 41: 1–14). Although AIDS currently represents the most prevalent immunocompromising disease of humans, a variety of other conditions or medical treatments can impair the human immune system and create susceptibility to diseases caused by the primary pathogen H. capsulatum and associated opportunistic pathogens (Goodwin et al., 1981, Medicine (Baltimore) 60: 231–266). These predisposing conditions include advanced age, diabetes, cancer chemotherapy, or immunosuppression induced to prevent rejection of transplanted organs (Wheat et al., 1982, Ann. Intern. Med., 96: 159–163; Davies et al., 1978, Am. J. Med. 64: 94–100).
In nature, H. capsulatum exists as a mycelium that is well-adapted for a saprotrophic mode of growth in soil (Scherr & Weaver, 1953, Bact. Rev. 17: 51–92). After entrance of microconidia or mycelial fragments into a mammalian host, H. capsulatum differentiates into budding yeast (Maresca et al., 1994, Trends Microbiol., 2: 110–114). In the animal host, the fungus experiences significant host-induced or environmental stress, including heat shock, exposure to higher osmolarity, changes in pH, and oxidative stress (Deepe, 1994, J. Lab. Clin. Med. 123: 201–205; Eissenberg & Goldman, 1994, The Interplay Between Histoplasma Capsulatum and Its Host Cells, Vol, I, Ch. 6, W. B. Saunders Company, Ltd., London, UK; Newman, 1999, Trends Microbiol., 7: 67–71). The ability to resist or overcome environmental or host-induced stress is likely to be important for continued growth and virulence of H. capsulatum. In addition, host-induced or environmental stress may trigger changes in gene expression necessary for virulence.
Most fungi share considerable similarities at the nucleic acid and/or protein level. For example, there is considerable sequence identity for fungi rRNA at the sequence level. The ability to distinguish among various fungi may be of considerable importance clinically (Kasuga, T., et al., 1999, J. Clin Micro., 37: 653–663). For example, H. capsulatum requires different clinical treatment than other fungal pathogens (Li, R-K., et al., 2000, Antimicrobial Agents, 44: 1734–1736; D. K. Stein and A. M. Sugar, 1989, Diagn. Microbiol., Infect., Dis., 12: 221S–228S; Ampel, 1996). In the case of individuals with AIDS, it is essential that infections resulting in disseminated histoplasmosis be rapidly diagnosed so that appropriate treatment can be undertaken to obtain the most favorable outcome. Thus, there is a need to distinguish between H. capsulatum and other fungi.
There is also a specific need to distinguish between H. capsulatum and the closely related organism, Blastomyces dermititidis. Although B. dermititidis is also an aggressive pathogen, H. capsulatum infection requires a different clinical treatment than infection with B. dermititidis (Li, R-K., et al., 2000; Ampel, 1996). Previous work indicates there is a high level of genetic similarity between H. capsulatum and B. dermatitis. For example, it has been shown that antibodies raised against H. capsulatum M antigen cross react with a similar sized protein in B. dermatititis (Hamilton, A. J. et al., 1990, J. Med. Vet. Mycol., 28: 479–485). Therefore, there is a need to identify differences at the genomic level for the development of sequence-specific assays that will be able to differentiate these two closely related organisms.
A major structural component found in fungi and plants that is lacking from many other eukaryotic cells, is a cell wall. In fungi, the cell wall performs a complex set of function (see e.g., C. A. Munro and N. A. R. Gow, 2001, Medical Mycology, 39 (S1), 41–53) including providing a skeletal scaffolding where important cell surface components can be docked, as well as protecting the cell from external toxic threats. Major components of the cell wall include (1-3)-β-D-glucan and chitin. The amount of chitin found in the cell wall varies widely among various species of fungi. Little is known concerning the content and biosynthesis of the chitin component of the cell wall of H. capsulatum, as characterization of cell wall chitin has primarily focused on Saccharomyces cerevisiae. 
To date, six classes of chitin synthases have been identified in fungi. Class III, V, and VI chitin synthases have been found to be unique to the filamentous fungi. Functionally, class I, II, and III synthases are believed to maintain the bulk of the housekeeping synthesis activities, while the enzymes of the remaining three classes (chitin synthases IV, V, and VI) have more specialized functions. In the case of the filamentous fungi, the class III synthases are believed to be responsible for synthesizing chitin for cell wall biogenesis which occurs during filamentous growth. In many cases, elimination of a single chitin synthase gene function results in little change in phenotype. Still, for at least some double mutants, such as in the case of the chs2 and chs3 double mutant in Wangiella dermatitidis, loss of these chitin synthase genes is associated with a significant decrease in virulence. These two chitin synthase genes are of the class I (chs2) and III (chs3) variety, respectively. Thus, multiple gene disruptions within the first three classes of chitin synthase genes is generally associated with significant reductions in chitin content in the cell wall and can contribute to decreased levels of virulence.
Thus, there is a need for the development of methods which specifically detect H. capsulatum in humans. There is also a need to be able to distinguish this pathogen from other fungi, especially closely related pathogens, such as Blastomyces dermititidis. There is also need to distinguish a latent H. capsulatum infection from an ongoing case of histoplasmosis. The ability to closely monitor this disease in high risk populations will enable the development of early treatment protocols suitable for patients, such as immunosuppressed individuals, who may not be able to defend against advanced stages of infection.